Higher amounts of testosterone and naturally greater percentage of muscle mass. Women require a higher percentage of body fat to support reproduction so our amount of muscle mass is less when compared to males.
Men produce larger amounts of testosterone which is what supports muscle growth and recovery.
Even if a woman did a more intense workout than Pilates and light weights, it would still take a little more time than a male to build the muscle.
Last I heard, it was testosterone, and body shape. Women tend to get wider in the hips (makes birthing much easier) whereas men can get wider shoulders. A male body is (generally, of course. Exceptions all around) able to better proportion the muscle.
Also, a lot of women don't seem to lift heavy enough. I know a few women who are scared they'll look like men if they lift something heavier than a gallon of milk.
There's obvious reason like others have posted such as TESTOSTERONE, ACIDS and from common stuff is physical. A lot of men like to get 'big' where ladies like to be 'slim' or 'slender' I have a lot of friends who work out, some take it to different levels such as bodybuilding (both male and female) and others like myself focus on certain groups. I myself like having a bigger upper body, it has to do with being an 'Alpha Male' thing if your a bigger wolf your feared lol but it's true.